IPSCs and CRISPR

Asking new questions

New disease models

New targets

Speeding up drug discovery

Science

Getting closer to reality

Combining two Nobel Prize-winning tools into one, Rosemarie Ungricht and Philipp Hoppe and their team from the Novartis Institutes for BioMedical Research in Basel are pursuing cutting-edge biology with the goal to find novel ways to treat kidney diseases. Their approach was unthinkable just a few years ago and is providing another boost to drug discovery and chemical biology.

Text by Goran Mijuk, photos by Laurids Jensen

Preparation of kidney organoids.

Table of contents

IPSCs and CRISPR

Asking new questions

New disease models

New targets

Speeding up drug discovery

Published on 13/12/2022

The Lab of the Future at Fabrikstrasse 22 on the Novartis Campus in Basel is already 10 years old, which by today’s fast-moving standards in the world of science may feel like the distant past.

But the lab in the classy building from star architect David Chipperfield has lost nothing of its forward-looking ambition. The elegant stone encasing of the outer shell with its darkened windows breathes a classical sovereignty, which is matched by a relaxed coolness in the inside.

The labs themselves, with their open space comfort, are as contemporary and fresh as they were a decade ago. But, more importantly, the science that is pursued in this state-of-the-art research building is still very much dedicated to shaping the future of medicine.

One of the projects that was executed here with this grand scheme in mind was launched some five years ago when Rosemarie Ungricht and her colleague Philippe Hoppe thought of the possibility to combine the insights of induced pluripotent stem cell-derived organoids and gene scissor technology.

Their goal was to produce kidney organoids – mini-organs that act in a similar way to real ones – and knock out one gene after the other to better understand which genes are driving kidney biology and are responsible for certain kinds of diseases.

The underlying idea was to work with biological models that are closer to reality, which can provide researchers with clearer insights of how diseases evolve and find ways to block them in a very targeted fashion.

“We wanted to do genetic screening in a more relevant biological model,” says Philipp Hoppe, a stem cell biologist who joined the Novartis Institutes for BioMedical Research in 2015. “To do this, we started to work with kidney organoids, which have a three-dimensional structure that better reflects the real biology behind the actual organs.”

Rosemarie Ungricht checks the quality of the kidney organoids.

IPSCs and CRISPR

Ungricht and Hoppe tapped into induced pluripotent stem cell (iPSC) technology as well as CRISPR/Cas9, two tools that were awarded the Nobel Prize in the last decade and have catapulted medical research to levels hitherto deemed impossible. Stem cell research, which was an ethically challenging field for decades, got a major boost in 2006 when Japanese researcher Shinya Yamanaka found a way to transform simple cells back into stem cells, which have the ability to grow into all kinds of other cells without the need for any embryonic tissue.

Thanks to this technology, for which Yamanaka received the Nobel Prize in medicine in 2012, scientists can take a skin cell, for example, revert it into a stem cell, which then can be reprogrammed into a brain, heart or kidney cell.

By letting these cells grow, researchers can also generate organoids such as minibrains or minikidneys, which act akin to real organs. This has the huge advantage that researchers can study organ-specific cells in their 3D context, which otherwise would be difficult or impossible to do.

With the advent of CRISPR/Cas9, the field saw another breakthrough, as this gene-altering method trumped existing technologies such as zinc finger nucleases and TALENs in terms of both efficiency and precision.

Developed by Jennifer Doudna and Emmanuelle Charpentier in 2011, for which they received the Nobel Prize recently, the technology makes use of gene-slicing bacteria and allows scientists to cut and replace DNA in a very precise way.

The technology has not only led to a proliferation of gene research across the globe, given the tool’s scientific prowess and economic efficacy. It has also imbued the sector with fresh hopes after gene therapy hit a wall around the millennium.

The organoids are incubated during a specific period of time...

Asking new questions

For Ungricht and Hoppe, merging the two technologies was not only about using cutting-edge tools, but opening the doors of science to develop new approaches which were difficult to pursue with conventional techniques.

“Our method opens up a new space, because you can ask different questions,” says Rosemarie Ungricht, who initiated work on this project as part of her postdoc assignment, when she joined in 2017. “Since we’re using stem cells, we can recapitulate the fetal development of kidneys and can ask questions such as which genes are actually necessary to reach a certain development point.”

Such questions are not viable in standard cell models in which researchers use isolated cells. While cell-based studies are still useful in understanding basic cell mechanisms, organoids provide researchers with a much more realistic picture of the organ itself.

Furthermore, disease-relevant inquiries can also be pursued. “With this method, you can investigate important processes like communication between two different cell types that would happen upon a kidney injury, such as which genes influence this communication. And I think this is actually a new space that we open up with these model systems,” Hoppe said.

According to Hoppe, setting up the systems for both induced pluripotent stem cell-derived organoids and CRISPR/Cas9, although challenging, went relatively smoothly. Still, when the team launched its project, the outcome was far from clear.

“When we started this project as part of Rosi’s postdoc at Novartis, we simply didn’t know if this would work, because it had never been done before, especially not in the kidney space,” Hoppe said. “But thanks to a very elaborate technical setup, we were able to really answer different aspects of biology.”

...before being shipped to the drug discovery team.

New disease models

The organoids floating in the colored fluid may be an anticlimax to a layman, much like a muddied energy drink. But considering that the tiny floating specks are mini-organs that have been genetically reprogrammed, one needs to remind oneself that it took decades of hard research to achieve this.

No wonder that Ungricht and Hoppe are excited about what they were able to achieve in the past five years, culminating in a widely read research paper in Cell Stem Cell, which detailed their work with kidney organoids and their use of CRISPR to get a better understanding of the underlying biology.

But Hoppe and Ungricht didn’t stop there. Their research was also instrumental in shedding light on which genes are responsible for certain kidney diseases, providing them with new, more realistic disease models.

New targets

“Our method allows us to really look, in very high molecular detail, at which genes are expressed in individual cell types of those kidney organoids,” Hoppe said.

Furthermore, the team can now shine a light on individual disease models. “This means that if you know that a certain gene is relevant for a certain kidney disease, we can knock out this gene and recapitulate the disease in the dish to a certain extent. This is what we’re doing,” Hoppe explained.

So far, the team has produced a disease model for a monogenetic kidney disease, which is now being tested against chemical compounds. Ungricht and Hoppe believe that their way of working can also be used for different kinds of kidney disease and other organoid systems. “We are convinced that this system will really help us experimentally to come up with novel targets,” Ungricht said.

From a medical point of view, identifying novel targets would be more than welcome. According to the International Society of Nephrology, around 850 million people worldwide suffer from some form of kidney disease. And the number of affected patients is increasing every year.

The kidney organoids are tested against the chemical compound library. Robotic systems help speed up this process.

Speeding up drug discovery

The two are also optimistic that their approach could one day help speed up drug development times and increase the likelihood that early-stage compounds make it to the patient.

While they acknowledge that using organoids for chemical screening is a logistics challenge, the fact that the underlying disease models are more realistic puts the whole compound screening team in a better position to find potentially successful compounds.

Rather than taking all of the more than 1 million chemical structures stored in the Novartis compound library, Hoppe and Ungricht reduce this number by making educated guesses on those that have a higher likelihood of making an impact.

As a result, this could speed up drug development in the long term. “We hope to start with the right drug target, and the right drug candidate in the first place, which should increase the likelihood of more successful drug discovery programs,” Hoppe said.

To date, on average, out of some 100 early-stage compounds, only one makes it into a fully developed drug. “Of course, we would like to achieve a better ratio than we have now,” Hoppe said.

To get there, Hoppe and Ungricht said, the team will not only need time, but will also have to continue working on even more robust disease models. After creating some first organoid disease models, which already include more than a dozen different kinds of cell types, the team is also working on further developing the models.

“As we get closer to reality and get a better understanding of the underlying cause of disease in our models, this will be another important step in our effort to make drug discovery more efficient,” Hoppe said. “It’s a dream and it will take a long time. But chances that we can succeed in this respect are looking good.”

If successful, organoids would be a model for the future.

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